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IPAK BIOLOGY A

SYLLABUS - Fall 2024

This course starts September 21, 1pm ET

INSTRUCTOR: James Lyons-Weiler, PhD

Affiliations: IPAK/IPAK-EDU

Join Dr. Lyons-Weiler as he brings us on an exploration of the profound realities of living beings from subatomic influences to civilizations and entire ecosystems in IPAK-EDU’s Bio A and Bio B courses.

IPAK BIO 111 BIOLOGY A is a 15- week course in the fundamentals of Biological Sciences. This course is the first of two courses designed to teach the public the fundamentals of biology. The sister course, IPAK BIO 102/112 is offered in the alternative semester. IPAK BIO 101/111 is a pre-requisite for IPAK BIO 102/111 and other courses offered by IPAK-EDU.

Topic 1 - Course Overview. Overview of Life on Earth.

Lecture 1: The diversity and meaning of life.

From single-celled organisms to higher primates and humans, all of life shares on goal: to thrive and survive. Everything you will learn in this course is HOW living organisms on Earth achieve those goals. Carbon (for most). Energy (for all). Nutrients (all). Oxygen (mostly). Light for some, dark for others. Access to mates (for some). Knowing Biology is about knowing the details - and the exceptions. Science as a way of knowing. Hypothesis. What happens when things go wrong. Relevance to society today.

Concepts: Carbon and Water. Biomolecules. Cells. Acquiring Energy. Scientific method.

Topic 2 Cellular Biology

Lecture 2: The Amazing Living Cell: How Life Arranges and Rearranges Itself

Organisms from single-celled organisms to plants and animals separate themselves from their environment in a battle against entropy. Learn the various ways that life has solved the problem of sequestration of resources and how this has diversified into myriad cellular processes and functions. Cells are amazing; learn and overview of how they function. What happens when things go wrong. Relevance to society today.

Concepts: Cellular anatomy, processes and functions.

Topic 3 Membranes - the Thin Line Between Self and Non-Self

From an organisms’ viewpoint, everything external to “self” represents either an opportunity or a threat. Learn how cells keep the bad out and the good in. Learn how they use electrochemical charge to move materials around in cells and how that is related to transport across membranes. What happens when things go wrong. Relevance to society today.

Concepts: Membrane structure & function. Types of cells. Secretion. Cells that Migrate.

Topic 4 Cellular Energetics- Powering the Machinery of Life

It takes a lot of energy to drive a cell. Energy is stored and spent chemically. Enzymes (active and reactive proteins) perform an astounding diversity of types of work with amazing efficiency. They break down resources, tear down used parts, and build up part of cells. Some fold other proteins. Other biological reactions turn light into matter. What happens when things go wrong. Relevance to society today.

Concepts: Introduction to Metabolism. Enzymatic reactions. Metabolic pathways.

Topic 5 DNA to Proteins: Transcribing and Translating Life’s Code

Understanding how living organisms do everything they do depends on cracking the code of information on doing cellular business and transmitting that information between generations. All of the cellular parts are constructed on the basis of inherited information that must be transformed from DNA to amino acid sequences. How this happens is one of the most interesting aspects of life on earth. What happens when things go wrong. Relevance to society today.

Concepts: Transcription. Translational. Intracellular Transport.

Topic 6 Two or Eight Cells from One: The Cell Cycle

Our cells don’t last forever - so how do we renew them and keep fresh tissue around? Where do gametes (sperm and egg) come from? The cell cycle is a highly regulated process by which cells divide. In mitosis, we two cells are derived from one. In meiosis, eight cells derive from one. Along the way we see a choreographed ballet that rivals The Nutcracker. We’ll step through each stage and learn precisely what is going on at the molecular, subcellular and cellular level. We’ll explore how this is timed, the signals that cause cells to divide, and how through cellular division and signaling cells differentiate into specialized tissues. What happens when things go wrong. Relevance to society today.

Concepts: Mitosis and Meiosis. Cellular differentiation. Cellular division. How Mutations Occur.

Topic 7 Cellular Bioenergetics: How Cells Breathe - and Ferment

All cellular processes require energy. We will break down how cells break down compounds for energy into ATP. Along the way, you’ll learn about Oxidation and Reduction, which are essential to understanding and how cells breathe (Cellular Respiration: Reactions in a Row). How do cells get energy from sugars (answer: Glycolysis). Cells also employ a clever process called the

Citric Acid Cycle to release stored energy from carbohydrates, fats and proteins. What happens when things go wrong. Relevance to society today.

Concepts: Cellular Respiration and Fermentation

Topic 8 Turning Energy into Matter: Biology Meets Quantum Physics

Animals think they are so cool, but they can’t do what plants make look easy: turning sunlight into matter. How this happens is an incredible feat of nature. Photon trapping. The Light Dependent Reaction. The Light Independent Reaction. The Calvin Cycle

Concepts: Photosynthesis, Quantum Biology, Origins of Photosynthesis

What happens when things go wrong. Relevance to society today.

Topic 9 Genetics

The vertical transmission of information between generations was an innovation so profoundly genius - and essential to adaptation to local conditions that it is almost taken for granted. Imagine if offspring had to re-invent the solutions to life’s problems of acquiring energy, nutrients, etc. every generation? What would be the point of having parents? Gregor Mendel noticed patterns in the inheritance of features in peas that led him to the idea of particles, or packages of information, being inherited by offspring from parents. This ultimately led to the idea of a “gene”, which was soundly verified by biologists. The vertical transmission of information follows patterns that can be mapped on pedigrees.

Concepts. Chromosomal and molecular inheritance. Gene regulation. Epigenetics. Introduction to pedigrees. Genotypes. Phenotypes. Homo- and Heterozygosity.

What happens when things go wrong. Relevance to society today.

Topic 10. Epigenetics

Inter-generational inheritance of patterns of methylation helps organisms anticipate the situation into which they are born. Patterns of methylation determine gene expression patterns

What happens when things go wrong. Relevance to society today.

Topic 10. Microbial and Viral Biology

Viruses hijack their hosts for their replication needs. Use of another organisms’ body or tissue for access to nutrients is known as parasitism, thus viruses can be seen as obligate parasites. Microbes and viruses that cause disease do so at their own peril; a dead host is (usually) not useful to an infectious agent. Host species have evolved responses, including various types of immune responses to infection.

Concepts: Viral replication; microbial replication. Host:Pathogen relationships

What happens when things go wrong. Relevance to society today.

Topic 11. Reading Gene Sequences: PCR and DNA Variation Analysis

We and other organisms employ polymerase to make copies of DNA. Humans have managed to reproduce this process in the test tube to produce millions of copies of specific, targeted DNA sequences. This process is essential for understanding the genetic basis of disease, how genomes work, and how species are related to each other. In this section, we’ll review how PCR works; how we sequence RNA viral genomes, and look at some fascinating aspects of microbial biology revealed by sequence analysis. We’ll analyze a few sequences ourselves using some of the tools of Bioinformatics.

Concepts: Polymerase Chain Reaction; Reverse Transcript PCR; Microbial Point of Origin; GC-Skew

Concepts: Biotechnology, PCR, RT-PCR, Bioinformatics

Topic 12. Protein Biology

When organisms need proteins, they construct them from information encoded in DNA. How this takes place is fundamental to fully understanding cellular and organismal biology and disease. Proteins either take shape automatically or require assistance from other proteins to fold into the appropriate shape necessary to acquire its correct function. A highly conserved process called the unfolded protein response allows cells to resolve clogged intracellular compartments in any of three ways. We’ll review numerous types of proteins that perform vital functions to familiarize you with the diversity of forms of proteins that make us and all organisms viable.

Concepts: Protein folding, ER-Stress, unfolded protein response, Haemoglobin. Nucleases. Ubiquitination. Alternative splicing.

What happens when things go wrong. Relevance to society today.

Topic 13. Nutrition

You are what you eat - almost. Using the knowledge shared to date in the class, we will examine an overview of human nutrition. Proteins. Fats, Sugars. Nutrients. Co-Factors (Vitamins). Bad actor. The Human Microbiome. Balancing lifestyle and nutrition. Nutrition and health.

What happens when things go wrong. Relevance to society today.

Week 12 Gas and Fluid Transport

Oxygen and carbon dioxide transport across membranes and throughout the circulatory systems and organs. Other dissolved gases. Oxygen and wellness. Carbon dioxide toxicity. Carbon monoxide poisoning. Dissolved nutrients.

Concepts: Circulation, transport, gas exchange.

What happens when things go wrong. Relevance to society today.

Week 13 Neurobiology

Simple nervous systems exist that pulse information across a simple net. More complex nervous systems result from diversification of nerve cells and their relatives and specialization of function. Some spectacular feats of development place the parts of the developing nervous system in the right place - at the right time. We’ll explore the central nervous system (CNS) and the autonomous nervous system (ANS). How do nerve cells communicate? What is a thought? What is a memory?

What happens when things go wrong. Relevance to society today.

Week 14 Hormones: The Symphony of the Glands

Our bodies speak to themselves, with one part telling another part “it’s time to wake up”; “it’s time to go to sleep”; “it’s time to make sperm”; “it’s time to make milk”. These signals are part of our endocrine system - and we hardly realize when these signals get passed and are received. Scare someone, they will feel an adrenaline rush. Love someone, they feel endorphins. As organisms, we respond to these signals most naturally. Making sense of us requires more than understanding anatomy, where organs are located, and how neurons work. It requires an appreciation for the waves of states of being that pass through us, and make us and other animals (we presume) feel a certain way. Hormones are essential for brain function, sexual development, falling in love, and of course human reproduction cycles.

Concepts: Hormones. Cell-to-cell signalling. Receptors.

What happens when things go wrong. Relevance to society today.

Week 15 The Human Immune System (WIth Guest Speaker TBA)

The mammalian innate and adaptive immune systems are remarkable feats of evolutionary engineering. We’ll learn how the body reacts to initial infections, and how it learns to produce antibodies that can match just about any foreign antigen. We’ll look at common types of autoimmunity and study specific mechanisms of how and why an immune system can even turn on itself.

What happens when things go wrong. Relevance to society today.

Resources

https://courses.lumenlearning.com/suny-mcc-biology2/chapter/transport-of-gases-in-human-bodily-fluids/